A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources

Bin Ma, Caiyu Lu, Yiling Wang, Jingwen Yu, Kankan Zhao, Ran Xue, Hao Ren, Xiaofei Lv, Ronghui Pan, Jiabao Zhang, Yongguan Zhu and Jianming Xu ()
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Bin Ma: Zhejiang University
Caiyu Lu: Zhejiang University
Yiling Wang: Zhejiang University
Jingwen Yu: ZJU-Hangzhou Global Scientific and Technological Innovation Center
Kankan Zhao: Zhejiang University
Ran Xue: ZJU-Hangzhou Global Scientific and Technological Innovation Center
Hao Ren: ZJU-Hangzhou Global Scientific and Technological Innovation Center
Xiaofei Lv: China Jiliang University
Ronghui Pan: ZJU-Hangzhou Global Scientific and Technological Innovation Center
Jiabao Zhang: Chinese Academy of Sciences
Yongguan Zhu: Chinese Academy of Sciences
Jianming Xu: Zhejiang University

Nature Communications, 2023, vol. 14, issue 1, 1-14

Abstract: Abstract Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter, presenting an untapped reservoir of microbial biodiversity and genetic resources, but has yet to be fully explored. In this study, we conduct a large-scale excavation of soil microbial dark matter by reconstructing 40,039 metagenome-assembled genome bins (the SMAG catalogue) from 3304 soil metagenomes. We identify 16,530 of 21,077 species-level genome bins (SGBs) as unknown SGBs (uSGBs), which expand archaeal and bacterial diversity across the tree of life. We also illustrate the pivotal role of uSGBs in augmenting soil microbiome’s functional landscape and intra-species genome diversity, providing large proportions of the 43,169 biosynthetic gene clusters and 8545 CRISPR-Cas genes. Additionally, we determine that uSGBs contributed 84.6% of previously unexplored viral-host associations from the SMAG catalogue. The SMAG catalogue provides an useful genomic resource for further studies investigating soil microbial biodiversity and genetic resources.

Date: 2023
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DOI: 10.1038/s41467-023-43000-z

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